It is important to analyze the efficiency of agricultural water and land resources utilization in macro-regions from the perspective of synergistic inputs and “economic-social-ecological” benefits for the sustainability of agricultural production. The connotation of agricultural water and land resources use efficiency was clarified by combining the broad concept of water resources and the characteristics of “multiple inputs-multiple outputs” in agricultural production, the super slacks based measure (Super-SBM) model and super undesirable slacks based measure (Super-Undesirable-SBM) model were constructed by using data envelopment analysis to measure the production allocation efficiency. The Super-SBM model and Super-Undesirable-SBM model were used to measure the efficiency of agricultural water and land resources utilization of the concept. Agricultural water and land resources utilization efficiency without considering ecological benefits (WLUE), agricultural water and land resources utilization efficiency with considering ecological benefits (WLUEE), water resource utilization efficiency loss (WUEL) and arable land resource utilization efficiency loss (LUEL) were measured for 51 counties in the study area, taking the Shandong Yellow Diversion Irrigation District as an example. By comparing and analyzing the WLUE and WLUEE measurement results, WUEL and LUEL decomposition results, the characteristics of agricultural water and soil resource utilization and the size difference of the two resource utilization efficiency losses in each county of the study area were revealed, and the counties of the study area were classified into four types: green and efficient production type, ordinary efficient production type, green and inefficient production type and ordinary inefficient production type. The targeted improvement measures for agricultural soil and water resource use efficiency in each county and a perspective for the study of agricultural soil and water resource utilization efficiency were proposed. The research results were conducive to promoting the sustainable development of agricultural production in the study area.